Brian Ripley got me looking at the .Rprofile off list, and indeed, the problem originates from some subtle behavior of one package which I am still trying to understand. It doesn't appear to be a general problem, so let's consider this fixed (and it's probably not unique to Mac). If I find otherwise, I'll report back.
Thanks to all. Bryan On Nov 11, 2011, at 11:05 PM, Hadley Wickham wrote: > Try R --vanilla to see if it's a profile problem. > Hadley > > On Friday, November 11, 2011, Bryan Hanson <[email protected]> wrote: > > [a variation of this was posted on r-help the other day with no answers] > > > > I've done something to my installation and can't find the cause. This > > started up a few days ago, it could be related to the problem that Simon > > was working on in the past 48, but I increasingly think not. > > > > My current install is totally fresh this morning off of r.research.att.com > > and the problem persists. Here's a couple of examples: > > > > Example 1: > >> ?sd > > Error in help("sd", package = NULL) : > > could not find function "%is.not.a%" > > > > Example 2 (from r-help posting): > > > > I have 3 packages that I authored and they build and check just fine > > locally. However, when I try to install the local source packages (from > > the .tar.gz), I get the following message: > > > > Error in `+.POSIXt`(as.POSIXct(origin, tz = tz, ...), x) : > > could not find function "%is.a%" > > In addition: Warning message: > > In install.packages(file.choose(), .libPaths()[1], NULL, type = "source") : > > installation of package > > /Users/bryanhanson/Documents/Research/MetabolomicsProjects/ChemometricsStuff/BAHpackages/FuncMap_1.0-1.tar.gz > > had non-zero exit status > > > > Now this is pretty surprising to me; I don't use this function or any > > having to do with times or time series. I get the same message no matter > > which of the 3 packages I try to install locally. Further, if I go looking > > for whatever this function is, the following occurs, and no browser window > > opens: > > > >> findFn("is.a") > > found 3 matches > > Error in stopifnot(x %is.a% "POSIXct") : could not find function "%is.a%" > > > > Which is the same error as one gets just asking for help (Example 1), so I > > think that error is superceding any display of help pages. > > > > And a google search of the error message doesn't produce anything recent. > > > > Does anyone recognize this problem/error? I've thrown out and re-installed > > several times and it persists. I feel like it might be in a hidden file (I > > have not yet tried to remove all existing .Rhistory files). I also had a > > development version of ggplot2 installed a few days ago, in an attempt to > > fix a different problem. My current sessionInfo() is below. > > > > Thanks for any suggestions about where to look. Bryan > > *********** > > Bryan Hanson > > Professor of Chemistry & Biochemistry > > DePauw University > > > >> sessionInfo() > > R version 2.14.0 Patched (2011-11-09 r57624) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] graphics utils datasets grid grDevices stats methods > > base > > > > other attached packages: > > [1] HiveR_0.2-1 FuncMap_1.0-1 ChemoSpec_1.48-4 ggExtra_0.5.1 > > gridExtra_0.8.5 > > [6] GGally_0.3.1 stringr_0.5 ggplot2_0.8.9 proto_0.3-9.2 > > reshape_0.8.4 > > [11] plyr_1.6 sos_1.3-1 brew_1.0-6 xtable_1.6-0 > > rgl_0.92.798 > > > > loaded via a namespace (and not attached): > > [1] amap_0.8-7 bipartite_1.17 chemometrics_1.3.7 class_7.3-3 > > [5] e1071_1.6 igraph_0.5.5-3 lattice_0.20-0 MASS_7.3-16 > > [9] mclust_3.4.10 mvbutils_2.5.101 mvoutlier_1.9.4 > > mvtnorm_0.9-9991 > > [13] nnet_7.3-1 pcaPP_1.9-44 pls_2.2-0 R.oo_1.8.3 > > [17] R.utils_1.9.3 RColorBrewer_1.0-5 RFOC_2.0-02 > > robustbase_0.7-8 > > [21] rpart_3.1-50 seriation_1.0-6 sna_2.2-0 som_0.3-5 > > [25] splines_2.14.0 survival_2.36-10 tnet_3.0.5 tools_2.14.0 > > [29] TSP_1.0-5 vegan_2.0-1 > > > > _______________________________________________ > > R-SIG-Mac mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > > > -- > Assistant Professor / Dobelman Family Junior Chair > Department of Statistics / Rice University > http://had.co.nz/ [[alternative HTML version deleted]]
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